The complete chloroplast genome sequence of <i>Lirianthe hodgsonii</i>, a tree species of Magnoliaceae as least concern

Chen, Shaoyu; Tao, Wu; Ma, Huiqin; Fu, Yuhua; Zhu, Yong; Hao, Jiabo; Jiang, Hong; Sima, Yongkang

doi:10.1080/23802359.2020.1798296

Cited by 4 publications

(7 citation statements)

References 9 publications

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“…Among them, the rst group could be further divided into two secondary groups, including 11 species of Magnolia genus as the rst groups and Linriodendron genus as the second groups. The phylogenetic relationship of 14 species was mostly consistent with the study of Lirianthe hodgsonii [39][40]…”

Section: Divergence Time Estimation Based On Cp Complete Genomessupporting

confidence: 85%

Chloroplast genome and historical biogeography of the three Magnolias

Min

Guo

Yin

et al. 2021

Preprint

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Magnolia officinalis, M. officinalis subsp.biloba and M. hypoleuca are all typical medicinal plants, belonging to genus Magnolia and Family Magnoliaceae. Their molecular information, particularly genetic difference, were known less. In this study, the platform Illumina HiSeq was used to sequence and assemble a novel cp (chloroplast) genome of M. hypoleuca followed by cp purification. Combined with two published cp rawdata, gene cycles and function annotations were comparably performed for the three plant species. The results indicated that 19 791 019 clean reads was assembled for M. hypoleuca cp, Q30 being 91.33%, and genome 160 051 bp. Its GC content is 39.2%, including 37 tRNAs and 8 rRNAs. The M. hypoleuca had smaller chloroplast genome and more introns (or exons) than M. officinalis and M. officinalis subsp.biloba. And there were respectively 11 and 8 more functional genes in M. hypoleuca cp than that in the other two. Based on cp complete genomes sequences, we constructed the phylogenetic relationship and estimated the divergence time of the three species by ML (Maximum likelihood) method, with other 10 published Magnoliaceae species. The results showed that M. officinalis subsp.biloba and M. officinalis might diverge from M. hypoleuca around 18.98 Ma, then they diverged from each other around 15.00 Ma. Additionally, the middle Miocene warming period might play an important role in the demographic and evolutionary histories of the three Magnolias, which provided a novel insight of the origin and dispersal routes of M. hypoleuca.

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Section: Divergence Time Estimation Based On Cp Complete Genomessupporting

confidence: 85%

Chloroplast genome and historical biogeography of the three Magnolias

Min

Guo

Yin

et al. 2021

Preprint

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“…We had previously completed the assembly and annotation of chloroplasts of L. hodgsonii [ 23 ] and L. coco [ 30 ]. Here, we newly assembled the chloroplast genomes of six other Lirianthe species.…”

Section: Discussionmentioning

confidence: 99%

“…A total of 17 genera are recognized in Xia's system [6] and a total of 15 genera are recognized in Sima and Lu's system [7]. The system by Sima and Lu, based on the data on DNA and the observations of morphological characters, especially in living plants, is strongly supported by recent DNA work [21,23,30,32,41] and has been accepted by many scholars [11][12][13][14]. In order to better reflect the evolutionary steps and levels of Magnoliaceous plants, as well as the evolutionary trends and migration routes based primarily on morphological-geographical studies, it is a more feasible and useful approach to define smaller independent genera.…”

Section: Discussionmentioning

confidence: 99%

“…Earlier phylogenetics of Magnoliaceae plants based on DNA analysis employed from one to several nuclear or chloroplast DNA regions [ 20 , 21 , 22 ], but a recent systematic and phylogenetic study based on complete chloroplast genome (CPG) sequences of nine species of Lirianthe demonstrated that these nine species of Lirianthe form a monophyletic branch [ 23 ]. This study shows the value of chloroplast genomic data for systematic or species classification research, but did not include L. henryi , L. phanerophlebia , L. confusa , and L. brevisericea .…”

Section: Introductionmentioning

confidence: 99%

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Comparative Analysis of the Chloroplast Genomes of Eight Species of the Genus Lirianthe Spach with Its Generic Delimitation Implications

Wu,

Sima,

Chen

et al. 2024

IJMS

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Based on Sima and Lu’s system of the family Magnoliaceae, the genus Lirianthe Spach s. l. includes approximately 25 species, each with exceptional landscaping and horticultural or medical worth. Many of these plants are considered rare and are protected due to their endangered status. The limited knowledge of species within this genus and the absence of research on its chloroplast genome have greatly impeded studies on the relationship between its evolution and systematics. In this study, the chloroplast genomes of eight species from the genus Lirianthe were sequenced and analyzed, and their phylogenetic relationships with other genera of the family Magnoliaceae were also elucidated. The results showed that the chloroplast genome sizes of the eight Lirianthe species ranged from 159,548 to 159,833 bp. The genomes consisted of a large single-copy region, a small single-copy region, and a pair of inverted repeat sequences. The GC content was very similar across species. Gene annotation revealed that the chloroplast genomes contained 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes, totaling 130 genes. Codon usage analysis indicated that codon usage was highly conserved among the eight Lirianthe species. Repeat sequence analysis identified 42–49 microsatellite sequences, 16–18 tandem repeats, and 50 dispersed repeats, with microsatellite sequences being predominantly single-nucleotide repeats. DNA polymorphism analysis revealed 10 highly variable regions located in the large single-copy and small single-copy regions, among which rpl32-trnL, petA-psbJ, and trnH-psbA were the recommended candidate DNA barcodes for the genus Lirianthe species. The inverted repeat boundary regions show little variation between species and are generally conserved. The result of phylogenetic analysis confirmed that the genus Lirianthe s. l. is a monophyletic taxon and the most affinal to the genera, Talauma and Dugandiodendron, in Sima and Lu’s system and revealed that the genus Lirianthe s. s. is paraphyletic and the genus Talauma s. l. polyphyletic in Xia’s system, while Magnolia subsection Gwillimia is paraphyletic and subsection Blumiana polyphyletic in Figlar and Nooteboom’s system. Morphological studies found noticeable differences between Lirianthe species in aspects including leaf indumentum, stipule scars, floral orientation, tepal number, tepal texture, and fruit dehiscence. In summary, this study elucidated the chloroplast genome evolution within Lirianthe and laid a foundation for further systematic and taxonomic research on this genus.

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“…To reveal the evolutionary position of M. ventii among Magnoliaceae, M. ventii and the previously reported 45 cp genomes were aligned to the chloroplast genome matrix using MAFFT v7.487 (Katoh and Standley 2013 ; Chen et al. 2020 ; Sima et al. 2021 ) for ML analysis was based on the TVM + F+R2 model (Kalyaanamoorthy et al.…”

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confidence: 99%

The complete chloroplast genome and phylogenetic analysis ofManglietia ventii(Magnoliaceae)

Wang

2022

Mitochondrial DNA Part B

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Manglietia ventii is a highly ornamental timber tree species that is listed as endangered on the IUCN Red List. This study was conducted on the complete chloroplast genome of M. ventii. The length of the chloroplast genome is 159,950 bp with GC content as 39.3%. One hundred and thirty-one functional genes were identified in the genome, which included 86 protein-coding genes (PCGs), 37 tRNA genes, and eight rRNA genes. The phylogenetic analysis indicated that M. ventii is most closely related to M. megaphylla and M. aromatica , and the study provides new insights into the evolution of the Magnoliaceae.

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The complete chloroplast genome sequence of Lirianthe hodgsonii, a tree species of Magnoliaceae as least concern

Cited by 4 publications

References 9 publications

Chloroplast genome and historical biogeography of the three Magnolias

Chloroplast genome and historical biogeography of the three Magnolias

Comparative Analysis of the Chloroplast Genomes of Eight Species of the Genus Lirianthe Spach with Its Generic Delimitation Implications

The complete chloroplast genome and phylogenetic analysis ofManglietia ventii(Magnoliaceae)

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